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Choosing a Genome Browser for a Model Organism Database: Surveying the Maize Community Taner Z Genetics, Development and Cell Biology Genetics, Development and Cell Biology Publications 2010 Choosing a genome browser for a Model Organism Database: surveying the Maize community Taner Z. Sen Iowa State University, [email protected] Lisa C. Harper United States Department of Agriculture Mary L. Schaeffer United States Department of Agriculture Carson M. Andorf United States Department of Agriculture, [email protected] Trent E. Seigfried UFonitlloedw St thiatess D aepndar atmddenitt ofion Agalric wulorktures at: http://lib.dr.iastate.edu/gdcb_las_pubs Part of the Agriculture Commons, Bioinformatics Commons, Computational Biology See next page for additional authors Commons, and the Plant Breeding and Genetics Commons The ompc lete bibliographic information for this item can be found at http://lib.dr.iastate.edu/ gdcb_las_pubs/25. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Article is brought to you for free and open access by the Genetics, Development and Cell Biology at Iowa State University Digital Repository. It has been accepted for inclusion in Genetics, Development and Cell Biology Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Choosing a genome browser for a Model Organism Database: surveying the Maize community Abstract As the B73 maize genome sequencing project neared completion, MaizeGDB began to integrate a graphical genome browser with its existing web interface and database. To ensure that maize researchers would optimally benefit from the potential addition of a genome browser to the existing MaizeGDB resource, personnel at MaizeGDB surveyed researchers’ needs. Collected data indicate that existing genome browsers for maize were inadequate and suggest implementation of a browser with quick interface and intuitive tools would meet most researchers’ needs. Here, we document the survey’s outcomes, review functionalities of available genome browser software platforms and offer our rationale for choosing the GBrowse software suite for MaizeGDB. Because the genome as represented within the MaizeGDB Genome Browser is tied to detailed phenotypic data, molecular marker information, available stocks, etc., the MaizeGDB Genome Browser represents a novel mechanism by which the researchers can leverage maize sequence information toward crop improvement directly. Disciplines Agriculture | Bioinformatics | Computational Biology | Plant Breeding and Genetics Comments This article is from Database 2010 (2010): baq007, doi:10.1093/database/baq007. Rights Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The onc tent of this document is not copyrighted. Authors Taner Z. Sen, Lisa C. Harper, Mary L. Schaeffer, Carson M. Andorf, Trent E. Seigfried, Darwin A. Campbell, and Carolyn J. Lawrence This article is available at Iowa State University Digital Repository: http://lib.dr.iastate.edu/gdcb_las_pubs/25 Database, Vol. 2010, Article ID baq007, doi:10.1093/database/baq007 ............................................................................................................................................................................................................................................................................................. Original article Choosing a genome browser for a Model Organism Database: surveying the Maize community 1,2, 3,4 5,6 1 1 Taner Z. Sen *, Lisa C. Harper , Mary L. Schaeffer , Carson M. Andorf , Trent E. Seigfried , Downloaded from Darwin A. Campbell1 and Carolyn J. Lawrence1,2 1USDA-ARS Corn Insects and Crop Genetics Research Unit, 2Department of Genetics, Development and Cell Biology, Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, 3USDA-ARS Plant Gene Expression Center, 800 Buchanan Street, Albany, CA 94710, 4Department of Molecular and Biology, University of California Berkeley, Berkeley, CA 94720, 5USDA-ARS Plant Genetics Research Unit and 6Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA http://database.oxfordjournals.org/ *Corresponding author: Tel: +1 515 294 5326; Fax: +1 515 294 8280; Email: [email protected] Submitted 16 November 2009; Revised 8 March 2010; Accepted 9 March 2010 ............................................................................................................................................................................................................................................................................................. As the B73 maize genome sequencing project neared completion, MaizeGDB began to integrate a graphical genome browser with its existing web interface and database. To ensure that maize researchers would optimally benefit from the potential addition of a genome browser to the existing MaizeGDB resource, personnel at MaizeGDB surveyed research- ers’ needs. Collected data indicate that existing genome browsers for maize were inadequate and suggest implementation at Iowa State University on December 7, 2015 of a browser with quick interface and intuitive tools would meet most researchers’ needs. Here, we document the survey’s outcomes, review functionalities of available genome browser software platforms and offer our rationale for choosing the GBrowse software suite for MaizeGDB. Because the genome as represented within the MaizeGDB Genome Browser is tied to detailed phenotypic data, molecular marker information, available stocks, etc., the MaizeGDB Genome Browser represents a novel mechanism by which the researchers can leverage maize sequence information toward crop improvement directly. Database URL: http://gbrowse.maizegdb.org/ ............................................................................................................................................................................................................................................................................................. Introduction visualizing sequence-based data alongside genetic and phenotypic information. A genome browser is to genomic sequence data as a web Community resources including Model Organism browser is to the World Wide Web: both offer logical access Databases (MODs) [e.g. TAIR (1), FlyBase (2), etc.], to datastreams that are otherwise unintelligible. With the Clade-Oriented Databases (CODs) [e.g. Gramene (3), SGN advent of new DNA sequencing technologies and the avail- (4), etc.], Automatic Annotation Shops [e.g. PlantGDB (5), ability of copious amounts of sequence-based data from JCVI (6, 7), etc.] and others have a responsibility to provide many species, genome browsers have been developed as timely access to sequence data well-integrated with exist- a means for researchers to view, interact with, search ing traditional biological data. Determining how best to through and display sequenced genomes as well as to com- choose genome browser software to meet the needs of pare syntenic or similar regions of genomes among related users within the context of a group’s maintenance capabil- species. Various genome browsers have been created over ities is a major challenge for the groups working to the years, each with particular strengths and weaknesses. build and maintain these community resources. Described Many provide independent solutions for integrating and here are the methodologies we used to determine which ............................................................................................................................................................................................................................................................................................. Published by Oxford University Press 2010. This is Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http:// creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Page 1 of 9 (page number not for citation purposes) Original article Database, Vol. 2010, Article ID baq007, doi:10.1093/database/baq007 ............................................................................................................................................................................................................................................................................................. genome browser to implement at MaizeGDB (8–10), development), and direct interaction with individual re- the MOD for maize. searchers. Other databases, such as TAIR (1) and SGN (4) also rely on similar means to interact with and receive feed- The need for a genome browser at MaizeGDB back from their communities. However, to the best of our These are exciting times for maize researchers and breed- knowledge, the MaizeGDB Working Group is fairly unique ers. Not only is maize a major crop worldwide; a reference for a few reasons: the group (i) meets at least once yearly: genome sequence for the inbred line, B73, has been many other database groups’ advisory boards are formed released [www.maizesequence.org; (11)]. As of August then fail to meet, (ii) documents guidance online (see 2009, the minimum tiling path included 16 910 sequenced http://www.maizegdb.org/working_group.php) and (iii) Bacterial Artificial Chromosome (BAC) and fosmid clones routinely allows representatives
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